EzCatDB: M00161
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeM00161
CATH domainDomain 13.40.50.720 : Rossmann foldCatalytic domain
Domain 23.40.50.1770 : Rossmann foldCatalytic domain
Domain 3-.-.-.-
Domain 43.40.50.1220 : Rossmann foldCatalytic domain
E.C.1.6.1.2
MACiEM0116

CATH domainRelated DB codes (homologues)
3.40.50.1220 : Rossmann foldM00162,T00237,T00230
3.40.50.1770 : Rossmann foldD00031
3.40.50.720 : Rossmann foldS00543,S00551,S00552,S00553,S00602,S00604,S00605,S00608,S00610,S00625,S00319,S00328,S00329,S00330,S00331,S00332,D00456,D00457,D00458,S00324,S00320,S00325,S00326,S00327,D00459,S00335,S00336,S00334,T00219,S00339,D00513,D00001,D00002,D00003,D00005,D00007,D00008,D00010,D00012,D00017,D00018,D00023,D00027,D00028,D00031,D00032,D00033,D00034,D00035,D00037,D00048,D00071,D00476,D00481,D00482,D00490,D00492,D00494,D00545,D00601,D00603,D00604,D00605,D00615,D00845,D00857,D00858,M00171,M00210,T00002,T00010,T00011,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
UniProtKBKEGG

Q2RSB2Q2RSB3Q2RSB4
Protein nameNAD(P) transhydrogenase subunit alpha part 1NAD(P) transhydrogenase subunit alpha part 2NAD(P) transhydrogenase subunit betaNAD(P)+ transhydrogenase (AB-specific)
pyridine nucleotide transhydrogenase
transhydrogenase
NAD(P)+ transhydrogenase
nicotinamide adenine dinucleotide (phosphate) transhydrogenase
NAD+ transhydrogenase
NADH transhydrogenase
nicotinamide nucleotide transhydrogenase
NADPH-NAD+ transhydrogenase
pyridine nucleotide transferase
NADPH-NAD+ oxidoreductase
NADH-NADP+-transhydrogenase
NADPH:NAD+ transhydrogenase
H+-Thase
energy-linked transhydrogenase
NAD(P)+ transhydrogenase (AB-specific)
SynonymsEC 1.6.1.2
Nicotinamide nucleotide transhydrogenase subunit alpha 1
Proton-translocating transhydrogenase component 1
Pyridine nucleotide transhydrogenase subunit alpha 1
dI
EC 1.6.1.2
Nicotinamide nucleotide transhydrogenase subunit alpha 2
Proton-translocating transhydrogenase component 2
Pyridine nucleotide transhydrogenase subunit alpha 2
dII
EC 1.6.1.2
Nicotinamide nucleotide transhydrogenase subunit beta
Proton-translocating transhydrogenase NADP(H)-binding component
Pyridine nucleotide transhydrogenase subunit beta
dIII
RefSeqYP_427270.1 (Protein)
NC_007643.1 (DNA/RNA sequence)
YP_427269.1 (Protein)
NC_007643.1 (DNA/RNA sequence)
YP_427268.1 (Protein)
NC_007643.1 (DNA/RNA sequence)
PfamPF01262 (AlaDh_PNT_C)
PF05222 (AlaDh_PNT_N)
[Graphical view]
PF12769 (DUF3814)
[Graphical view]
PF02233 (PNTB)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00760Nicotinate and nicotinamide metabolism

UniProtKB:Accession NumberQ2RSB2Q2RSB3Q2RSB4
Entry namePNTAA_RHORTPNTAB_RHORTPNTB_RHORT
ActivityNADPH + NAD(+) = NADP(+) + NADH.NADPH + NAD(+) = NADP(+) + NADH.NADPH + NAD(+) = NADP(+) + NADH.
SubunitComplex of an alpha and a beta chain, in Rhodospirillum, the alpha chain seems to be made of two subunits (By similarity).Complex of an alpha and a beta chain, in Rhodospirillum, the alpha chain seems to be made of two subunits (By similarity).Complex of an alpha and a beta chain, in Rhodospirillum, the alpha chain seems to be made of two subunits (By similarity).
Subcellular location
Cell inner membrane, Multi-pass membrane protein (By similarity).Cell inner membrane, Multi-pass membrane protein (By similarity).
Cofactor



Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00005C00003C00006C00004
CompoundNADPHNAD+NADP+NADH
Typeamide group,amine group,nucleotideamide group,amine group,nucleotideamide group,amine group,nucleotideamide group,amine group,nucleotide
ChEBI16474
15846
18009
16908
PubChem5884
5893
5886
439153
            
1f8gA01UnboundBound:NADUnboundUnbound
1f8gB01UnboundAnalogue:NADUnboundUnbound
1f8gC01UnboundAnalogue:NADUnboundUnbound
1f8gD01UnboundBound:NADUnboundUnbound
1l7dA01UnboundUnboundUnboundUnbound
1l7dB01UnboundUnboundUnboundUnbound
1l7dC01UnboundUnboundUnboundUnbound
1l7dD01UnboundUnboundUnboundUnbound
1l7eA01UnboundUnboundUnboundBound:NAI
1l7eB01UnboundUnboundUnboundUnbound
1l7eC01UnboundUnboundUnboundUnbound
1l7eD01UnboundUnboundUnboundBound:NAI
1hzzA01UnboundBound:NADUnboundUnbound
1hzzB01UnboundUnboundUnboundUnbound
1nm5A01UnboundBound:NADUnboundUnbound
1nm5B01UnboundAnalogue:NADUnboundUnbound
1ptjA01UnboundUnboundUnboundUnbound
1ptjB01UnboundAnalogue:SNDUnboundUnbound
1u28A01UnboundBound:NADUnboundUnbound
1u28B01UnboundAnalogue:NADUnboundUnbound
1u2dA01UnboundBound:NADUnboundUnbound
1u2dB01UnboundBound:NADUnboundUnbound
1u2gA01UnboundAnalogue:APRUnboundUnbound
1u2gB01UnboundAnalogue:APRUnboundUnbound
1f8gA02UnboundUnboundUnboundUnbound
1f8gB02UnboundUnboundUnboundUnbound
1f8gC02UnboundUnboundUnboundUnbound
1f8gD02UnboundUnboundUnboundUnbound
1l7dA02UnboundUnboundUnboundUnbound
1l7dB02UnboundUnboundUnboundUnbound
1l7dC02UnboundUnboundUnboundUnbound
1l7dD02UnboundUnboundUnboundUnbound
1l7eA02UnboundUnboundUnboundUnbound
1l7eB02UnboundUnboundUnboundUnbound
1l7eC02UnboundUnboundUnboundUnbound
1l7eD02UnboundUnboundUnboundUnbound
1hzzA02UnboundUnboundUnboundUnbound
1hzzB02UnboundUnboundUnboundUnbound
1nm5A02UnboundUnboundUnboundUnbound
1nm5B02UnboundUnboundUnboundUnbound
1ptjA02UnboundUnboundUnboundUnbound
1ptjB02UnboundUnboundUnboundUnbound
1u28A02UnboundUnboundUnboundUnbound
1u28B02UnboundUnboundUnboundUnbound
1u2dA02UnboundUnboundUnboundUnbound
1u2dB02UnboundUnboundUnboundUnbound
1u2gA02UnboundUnboundUnboundUnbound
1u2gB02UnboundUnboundUnboundUnbound
1e3tAUnboundUnboundBound:NAPUnbound
1pnoAUnboundUnboundBound:NAPUnbound
1pnoBUnboundUnboundBound:NAPUnbound
1pnqABound:NDPUnboundUnboundUnbound
1pnqBBound:NDPUnboundUnboundUnbound
1hzzCUnboundUnboundBound:NAPUnbound
1nm5CUnboundUnboundBound:NAPUnbound
1ptjCUnboundUnboundBound:NAPUnbound
1u28CUnboundUnboundBound:NAPUnbound
1u2dCBound:NDPUnboundUnboundUnbound
1u2gCBound:NDPUnboundUnboundUnbound

Active-site residues
resource
literature [6], [10] & [12]
pdbCatalytic residuescomment
          
1f8gA01TYR  235
 
1f8gB01TYR  235
 
1f8gC01TYR  235
 
1f8gD01TYR  235
 
1l7dA01        
invisible Y235
1l7dB01        
invisible Y235
1l7dC01        
invisible Y235
1l7dD01        
invisible Y235
1l7eA01TYR  235
 
1l7eB01        
invisible Y635
1l7eC01        
invisible Y1035
1l7eD01TYR 1435
 
1hzzA01TYR  235
 
1hzzB01        
invisible Y235
1nm5A01        
invisible Y235
1nm5B01        
invisible Y235
1ptjA01TYR  235
 
1ptjB01        
invisible Y235
1u28A01TYR  235
 
1u28B01        
invisible Y235
1u2dA01TYR  235
 
1u2dB01TYR  235
 
1u2gA01TYR  235
 
1u2gB01        
invisible Y235
1f8gA02ARG  127;GLN  132;ASP  135;SER  138
 
1f8gB02ARG  127;GLN  132;ASP  135;SER  138
 
1f8gC02ARG  127;GLN  132;ASP  135;SER  138
 
1f8gD02ARG  127;GLN  132;ASP  135;SER  138
 
1l7dA02ARG  127;GLN  132;ASP  135;SER  138
 
1l7dB02ARG  527;GLN  532;ASP  535;SER  538
 
1l7dC02ARG  927;GLN  932;ASP  935;SER  938
 
1l7dD02ARG 1327;GLN 1332;ASP 1335;SER 1338
 
1l7eA02ARG  127;GLN  132;ASP  135;SER  138
 
1l7eB02ARG  527;GLN  532;ASP  535;SER  538
 
1l7eC02ARG  927;GLN  932;ASP  935;SER  938
 
1l7eD02ARG 1327;GLN 1332;ASP 1335;SER 1338
 
1hzzA02ARG  127;GLN  132;ASP  135;SER  138
 
1hzzB02ARG  127;GLN  132;ASP  135;SER  138
 
1nm5A02ARG  127;        ;ASP  135;SER  138
mutant Q132N
1nm5B02ARG  127;        ;ASP  135;SER  138
mutant Q132N
1ptjA02ARG  127;GLN  132;ASP  135;SER  138
 
1ptjB02ARG  127;GLN  132;ASP  135;SER  138
 
1u28A02ARG  127;GLN  132;ASP  135;SER  138
 
1u28B02ARG  127;GLN  132;ASP  135;SER  138
 
1u2dA02ARG  127;GLN  132;ASP  135;SER  138
 
1u2dB02ARG  127;GLN  132;ASP  135;SER  138
 
1u2gA02ARG  127;GLN  132;ASP  135;SER  138
 
1u2gB02ARG  127;GLN  132;ASP  135;SER  138
 
1e3tATYR  55;ARG  90;TYR  171
 
1pnoATYR 316;ARG 351;TYR  432
 
1pnoBTYR 316;ARG 351;TYR  432
 
1pnqATYR 316;ARG 351;TYR  432
 
1pnqBTYR 316;ARG 351;TYR  432
 
1hzzCTYR  55;ARG  90;TYR  171
 
1nm5CTYR  55;ARG  90;TYR  171
 
1ptjCTYR  55;ARG  90;TYR  171
 
1u28CTYR  55;ARG  90;TYR  171
 
1u2dCTYR  55;ARG  90;TYR  171
 
1u2gCTYR  55;ARG  90;TYR  171
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]p.5-6
[10]p.813
[12]p.44759-44760
[13]p.30684-30685
[14]p.167-173
[16]

[17]Fig.8, p.12152
[18]p.1223-1225
[19]

[21]

[22]


references
[1]
PubMed ID8011636
JournalBiochemistry
Year1994
Volume33
Pages7691-700
AuthorsHolmberg E, Olausson T, Hultman T, Rydstrom J, Ahmad S, Glavas NA, Bragg PD
TitlePrediction and site-specific mutagenesis of residues in transmembrane alpha-helices of proton-pumping nicotinamide nucleotide transhydrogenases from Escherichia coli and bovine heart mitochondria.
[2]
PubMed ID9804876
JournalBiochim Biophys Acta
Year1998
Volume1409
Pages25-38
AuthorsGupta S, Quirk PG, Venning JD, Slade J, Bizouarn T, Grimley RL, Cotton NP, Jackson JB
TitleMutation of amino acid residues in the mobile loop region of the NAD(H)-binding domain of proton-translocating transhydrogenase.
[3]
PubMed ID10393090
JournalBiochem J
Year1999
Volume341
Pages329-37
AuthorsVenning JD, Jackson JB
TitleA shift in the equilibrium constant at the catalytic site of proton-translocating transhydrogenase: significance for a 'binding-change' mechanism.
[4]
PubMed ID10514549
JournalBiochim Biophys Acta
Year1999
Volume1413
Pages81-91
AuthorsPeake SJ, Venning JD, Cotton NP, Jackson JB
TitleEvidence for the stabilization of NADPH relative to NADP(+) on the dIII components of proton-translocating transhydrogenases from Homo sapiens and from Rhodospirillum rubrum by measurement of tryptophan fluorescence.
[5]
PubMed ID10216162
JournalBiochim Biophys Acta
Year1999
Volume1411
Pages159-69
AuthorsPeake SJ, Venning JD, Jackson JB
TitleA catalytically active complex formed from the recombinant dI protein of Rhodospirillum rubrum transhydrogenase, and the recombinant dIII protein of the human enzyme.
[6]
PubMed ID10611473
JournalFEBS Lett
Year1999
Volume464
Pages1-8
AuthorsJackson JB, Peake SJ, White SA
TitleStructure and mechanism of proton-translocating transhydrogenase.
[7]
PubMed ID10587945
JournalMicrob Comp Genomics
Year1999
Volume4
Pages173-86
AuthorsStudley WK, Yamaguchi M, Hatefi Y, Saier MH Jr
TitlePhylogenetic analyses of proton-translocating transhydrogenases.
[8]
CommentsNMR Structure
PubMed ID11004437
JournalBiochim Biophys Acta
Year2000
Volume1459
Pages248-57
AuthorsJeeves M, Smith KJ, Quirk PG, Cotton NP, Jackson JB
TitleSolution structure of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase from Rhodospirillum rubrum.
Related PDB1e3t
[9]
PubMed ID10747934
JournalJ Biol Chem
Year2000
Volume275
Pages19490-7
AuthorsVenning JD, Peake SJ, Quirk PG, Jackson JB
TitleStopped-flow reaction kinetics of recombinant components of proton-translocating transhydrogenase with physiological nucleotides.
[10]
PubMed ID10997900
JournalStructure Fold Des
Year2000
Volume8
Pages809-15
AuthorsBuckley PA, Baz Jackson J, Schneider T, White SA, Rice DW, Baker PJ
TitleProtein-protein recognition, hydride transfer and proton pumping in the transhydrogenase complex.
Related PDB1f8g
[11]
PubMed ID11231296
JournalEur J Biochem
Year2001
Volume268
Pages1430-8
AuthorsRodrigues DJ, Venning JD, Quirk PG, Jackson JB
TitleA change in ionization of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase regulates both hydride transfer and nucleotide release.
[12]
PubMed ID11577115
JournalJ Biol Chem
Year2001
Volume276
Pages44757-61
AuthorsPinheiro TJ, Venning JD, Jackson JB
TitleFast hydride transfer in proton-translocating transhydrogenase revealed in a rapid mixing continuous flow device.
[13]
PubMed ID11399770
JournalJ Biol Chem
Year2001
Volume276
Pages30678-85
AuthorsVenning JD, Rodrigues DJ, Weston CJ, Cotton NP, Quirk PG, Errington N, Finet S, White SA, Jackson JB
TitleThe heterotrimer of the membrane-peripheral components of transhydrogenase and the alternating-site mechanism of proton translocation.
[14]
PubMed ID11250201
JournalStructure (Camb)
Year2001
Volume9
Pages165-76
AuthorsCotton NP, White SA, Peake SJ, McSweeney S, Jackson JB
TitleThe crystal structure of an asymmetric complex of the two nucleotide binding components of proton-translocating transhydrogenase.
Related PDB1hzz
[15]
PubMed ID12206884
JournalBiochim Biophys Acta
Year2002
Volume1555
Pages8-13
AuthorsRodrigues DJ, Jackson JB
TitleA conformational change in the isolated NADP(H)-binding component (dIII) of transhydrogenase induced by low pH: a reflection of events during proton translocation by the complete enzyme?
[16]
PubMed ID12379117
JournalBiochemistry
Year2002
Volume41
Pages12745-54
AuthorsPrasad GS, Wahlberg M, Sridhar V, Sundaresan V, Yamaguchi M, Hatefi Y, Stout CD
TitleCrystal structures of transhydrogenase domain I with and without bound NADH.
Related PDB1l7d,1l7e
[17]
PubMed ID14567675
JournalBiochemistry
Year2003
Volume42
Pages12143-53
AuthorsSundaresan V, Yamaguchi M, Chartron J, Stout CD
TitleConformational change in the NADP(H) binding domain of transhydrogenase defines four states.
Related PDB1pno,1pnq
[18]
PubMed ID12564924
JournalBiochemistry
Year2003
Volume42
Pages1217-26
Authorsvan Boxel GI, Quirk PG, Cotton NP, White SA, Jackson JB
TitleGlutamine 132 in the NAD(H)-binding component of proton-translocating transhydrogenase tethers the nucleotides before hydride transfer.
Related PDB1nm5
[19]
PubMed ID12765762
JournalBiochim Biophys Acta
Year2003
Volume1604
Pages55-9
AuthorsPedersen A, Karlsson J, Althage M, Rydstrom J
TitleProperties of the apo-form of the NADP(H)-binding domain III of proton-pumping Escherichia coli transhydrogenase: implications for the reaction mechanism of the intact enzyme.
[20]
PubMed ID12972415
JournalJ Biol Chem
Year2003
Volume278
Pages47578-84
AuthorsBroos J, Gabellieri E, van Boxel GI, Jackson JB, Strambini GB
TitleTryptophan phosphorescence spectroscopy reveals that a domain in the NAD(H)-binding component (dI) of transhydrogenase from Rhodospirillum rubrum has an extremely rigid and conformationally homogeneous protein core.
[21]
CommentsX-ray crystallography
PubMed ID12791694
JournalJ Biol Chem
Year2003
Volume278
Pages33208-16
AuthorsSingh A, Venning JD, Quirk PG, van Boxel GI, Rodrigues DJ, White SA, Jackson JB
TitleInteractions between transhydrogenase and thio-nicotinamide Analogues of NAD(H) and NADP(H) underline the importance of nucleotide conformational changes in coupling to proton translocation.
Related PDB1pt9,1ptj
[22]
PubMed ID15323555
JournalBiochemistry
Year2004
Volume43
Pages10952-64
AuthorsMather OC, Singh A, van Boxel GI, White SA, Jackson JB
TitleActive-site conformational changes associated with hydride transfer in proton-translocating transhydrogenase.
Related PDB1u28,1u2d,1u2g,1u31

comments
This enzyme is composed of two alpha chains and a beta chain. Alpha-1 chain is homologous to the domain I (N-terminal matrix domain) of NAD(P)+ transhydrogenase from mammalian mitochondrial membrane (Swissprot P11024, Q13423; M00162 of EzCatDB), whilst beta chain is thomologous to the domain III (C-terminal matrix domain) of the counterpart enzyme. Although the tertiary structures of these chains have been solved, the structure of the remainder, alpha-2 subunit, which is a membrane-bound protein, has not been determined yet.

createdupdated
2004-12-172009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.